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- PDB-5w5q: MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-met... -

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Basic information

Entry
Database: PDB / ID: 5w5q
TitleMAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl-3-(5-methyloxazol-2-yl)but-1-yn-1-yl)-6,7-dihydro-5H-5,7-methanobenzo[c]imidazo[1,2-a]azepine-2,3-dicarboxamide)
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9X4 / Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å
AuthorsHarris, S.F. / Wu, P.
Citation
Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1).
Authors: Feng, J.A. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castanedo, G. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
#1: Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure based design of potent selective inhibitors of protein kinase D1 (PKD1)
Authors: Feng, J.W. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castaneda, G.M. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation_author
Revision 1.3Nov 13, 2019Group: Database references / Category: citation / citation_author
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase kinase 4
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1843
Polymers75,7402
Non-polymers4431
Water3,855214
1
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3142
Polymers37,8701
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)37,8701
Polymers37,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.611, 89.676, 90.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 4 / HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEKKK 4 / Nck-interacting kinase


Mass: 37870.078 Da / Num. of mol.: 2 / Fragment: UNP residues 2-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK / Production host: Escherichia coli (E. coli)
References: UniProt: O95819, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9X4 / (5s,7s)-N~3~-methyl-10-[3-methyl-3-(5-methyl-1,3-oxazol-2-yl)but-1-yn-1-yl]-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide


Mass: 443.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.33→90.65 Å / Num. obs: 28901 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 52.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 25.5 / Num. measured all: 188764 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.33-2.66.50.4475222180740.9430.1890.4864.5
5.2-90.656.20.01917312277410.0080.0270.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.33→59.95 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9233 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.39 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1457 5.08 %RANDOM
Rwork0.2095 ---
obs0.2108 28690 99.85 %-
Displacement parametersBiso max: 171.4 Å2 / Biso mean: 55.71 Å2 / Biso min: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1-10.2032 Å20 Å20 Å2
2---10.2195 Å20 Å2
3---0.0163 Å2
Refine analyzeLuzzati coordinate error obs: 0.327 Å
Refinement stepCycle: final / Resolution: 2.33→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 33 214 4996
Biso mean--37.14 48.37 -
Num. residues----588
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1761SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes121HARMONIC2
X-RAY DIFFRACTIONt_gen_planes730HARMONIC5
X-RAY DIFFRACTIONt_it4913HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion626SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5763SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4913HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6646HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.35
LS refinement shellResolution: 2.33→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2858 158 5.32 %
Rwork0.2306 2810 -
all0.2336 2968 -
obs--99.85 %

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